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Thursday, December 29, 2016

Wikipedia has a new animated gif of early Indo-European migrations (available at various resolutions here). It's pretty good overall, but very speculative and potentially erroneous in parts. For instance, my understanding is that the Vedic Aryans did not emerge from BMAC per se, as the map suggests, but rather from an post-BMAC phenomenon heavily influenced by steppe pastoralists. Hi-res ancient DNA from BMAC and post-BMAC sites should be able to resolve this issue.

As far as I know, BMAC remains were being tested at Harvard earlier this year, but the year is almost out, and nothing has been published. So either David Reich and co. are keeping the results for a new paper on the Indo-European homeland question, or they couldn't get any usable data from the samples. Keep in mind that only 30-40% of the ancient remains that are tested at Harvard are successfully genotyped. I can imagine that the success rate for samples from arid locations, like former BMAC sites in Turkmenistan, is even lower.
Update 31/12/2016: Commentator Tapatuevik Kaarmkyno points us to an article from earlier this year at NIH Record featuring this quote from David Reich:"We’ve sequenced more than 1,000 samples in our own lab — there’s not enough time to publish". That's probably why the second half of 2016 was so agonizingly slow. Next year should be awesome.
See also...
Maybe first direct hints of Yamnaya-related gene flow into South Central AsiaqpAdm tour of Europe: the Bronze Age invasion

Saturday, December 24, 2016

At least a couple of academic teams working on the population history of Europe need to read this PDF and take it to heart.

This article reviews scientific publications that have attempted to use genetic and genomic data in order to investigate European migrations between the fourth and ninth centuries. It considers early single-locus studies that used mtDNA and y-chromosome data. These studies were successful in formulating hypotheses concerning migration and heterogeneity, primarily between the Continent and the British Isles and Iceland, but could only examine a small portion of the entire genetic inheritance. The article continues with a presentation of more recent genome-wide studies. In particular, it evaluates the problems of using modern genomic data to understand past migratory processes, arguing that modern DNA is a problematic source for understanding population histories of the past fifteen hundred years and urges the sequencing and analysis of ancient DNA. It also presents some of the problems of re­search teams that did not include archaeologists and historians as integral participants in the planning, collection, and evaluation of data. It concludes with a brief outline of the authors’ current project that examines migration between Pannonia and Italy in the sixth century.
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This work is necessarily interdisciplinary, something notably lacking in the majority of genetic studies. The Ralph and Coop study, while highly rigorous at the level of the population genetic analysis, included no historians or archaeologists, and the only historical literature cited, presumably to »identify« the Hunnic contribution to European population, was a general history of Europe, [25] a survey of Slavic history, [26] and two articles in the New Cambridge Medieval History. [27] The Busby et al. study also included no historians or archaeologists on its team, and the only historical literature cited was a Penguin History of the World, Peter Heather’s survey of the Early Middle Ages, and a survey of Muslims in Italy. [28] Unlike these studies, designed and executed exclusively by geneticists who then look through a few general historical handbooks to try to find stories that might explain their data, historians and archaeologists are integrated from the start in our project.

Sunday, December 18, 2016

Danish archaeologist Kristian Kristiansen will have a paper out early next year in Antiquity Journal on the emergence of the Corded Ware Culture in Late Neolithic Northern Europe. His talk at the recent European Archaeologists Association (EAA) annual meeting was based on the forthcoming paper. Here's a Youtube clip of the talk.

There's a new preprint at bioRxiv about the spread of the plague across much of Eurasia via the expansions of Early Bronze Age steppe pastoralists. It's been up for a few days now. Judging by the number of tweets on the preprint, a lot of people have read it. Or have they?
The manuscript contains a glaring error, a couple times over, in which the authors mix up the Afanasievo Culture with the Andronovo Culture. That's OK, this is why we have preprints and bioRxiv. I just found it somewhat amusing to see one lonely voice pointing this out under the rash of tweets recommending the paper.

Update 20/12/2016: A corrected version of the preprint has just been posted at bioRxiv. See here.
See also...
Mobile and then some

Saturday, December 17, 2016

FTDNA has launched a new "Ancient Origins" analysis, and I've been asked a few times now what I think of the "Metal Age invader" component in this test. Essentially, I share the view of one of the commentators in the comments here.

FTDNA now models Europeans as a mix of hunter-gatherers (Loschbour, La Brana 1 and Motala), early European farmers (Stuttgart, Iceman, LBK) and so called "Metal Age invaders" which are based on Corded Ware and Yamnaya samples - so the latter is what we more typically call "steppe admixture". (Plus they add non-European admixture in case someone has it very evidently.) This model looks crude for our present-day standards, and their results look very different from what I've seen here in Davidski's analyses or in other ancient-DNA calculators on Gedmatch, as their inferred proportions of steppe admixture are much lower, about half of that inferred by others. And moreover to me it looks completely wrong that FTDNA suggests that I (1/4 Italian, strong southwest European component) have more Metal Age invader admixture than my fully East Prussian grandmother.

Indeed, any Early Bronze Age Steppe-inspired component should peak at 40-50% amongst Northern and Eastern Euros. This apparently doesn't. Why? No idea.
I know better than almost anyone else that there's no such thing as a perfect ancestry test, and FTDNA has every right to offer an experimental analysis to its clients, so let's leave it at that. But if you want to see what an ADMIXTURE test with a half-decent Yamnaya component looks like, then check out my attempt [HERE]. These are graphs from the linked blog entry showing inferred levels of Yamnaya-related ancestry proportions for Europeans and West Asians.

I've now read the new Valtuena et al. prerprint a couple of times, and even though the plague angle is interesting, what really sticks out for me is how incredibly mobile our steppe ancestors were.
It's been obvious for a while now that during the Early Bronze Age there was a massive expansion from the Pontic-Caspian Steppe in all directions, as far as the Atlantic shores in the west and the Altai region in the east. However, considering the phylogeny of Yersinia pestis genomes in Valtuena et al., it looks like the Yamnaya and/or closely related peoples also regularly roved across the entire length of the Eurasian Steppe.
The oldest and phylogenetically most basal sample of Yersinia pestis to date comes from an Afanasievo skeleton from the Altai region dated to 4836-4625 YBP. Hot on its heels, the next oldest is a sample derived from the Afanasievo strain, but from a Corded Ware skeleton from the East Baltic dated to 4571-4422 BP. The two burial sites are separated by something like 3,000 kilometers.
It's unlikely that Yersinia pestis spread from the Pontic-Caspian Steppe, say, with the Yamnaya, both to the Altai region and the East Baltic, because it hasn't yet been found in any of the Yamnaya remains. It's also generally accepted that Yersinia pestis is indeed from Asia. So it must have been picked up by migrants from the Pontic-Caspian Steppe somewhere in Asia, probably the Altai region, whose descendants then returned to Europe with the bug, and may have taken part in the Corded Ware expansion.
But of course it doesn't end there, because it appears that the descendants or close relatives of the Baltic Corded Ware people then moved back to Asia, because a sample of Yersinia pestis derived from the Corded Ware strain is found in an Andronovo skeleton from the Altai region dated to 3694-3575 BP. Note also that the genome-wide genetic structure of most of the Andronovo individuals sampled to date is Corded Ware-like, in fact more so than Yamnaya-like. In other words, ancient human DNA also shows a very close relationship between Andronovo and the older Corded Ware.
Why were these people roving around so much? I know they were pastoralists and that the Eurasian Steppe became progressively drier during the Bronze Age, so it may have been necessary to move wherever suitable pastures were available. But still, it seems rather ridiculous that they spent so much energy on long range intercontinental travel when, by all accounts, all they had were wagons pulled by oxen.
Citation...
Valtuena et al., The Stone Age Plague: 1000 years of Persistence in Eurasia, bioRxiv, Posted December 15, 2016. doi: https://doi.org/10.1101/094243
See also...
So how many of you really read the preprints at bioRxiv?Bronze Age dope dealers

Thursday, December 15, 2016

Abstract: Molecular signatures of Yersinia pestis were recently identified in prehistoric Eurasian individuals, thus suggesting Y. pestis might have caused some form of plague in humans prior to the first historically documented pandemic. Here, we present four new Y. pestis genomes from the European Late Neolithic and Bronze Age (LNBA) dating from 4,500 to 3,700 BP. We show that all currently investigated LNBA strains form a single genetic clade in the Y. pestis phylogeny that appears to be extinct today. Interpreting our data within the context of recent ancient human genomic evidence, which suggests an increase in human mobility during the LNBA, we propose a possible scenario for the spread of Y. pestis during the LNBA: Y. pestis may have entered Europe from Central Eurasia during an expansion of steppe pastoralists, possibly persisted within Europe until the mid Bronze Age, and moved back towards Central Eurasia in subsequent human population movements.
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The first indication of plague in Europe is found in the Baltic region and coincides with the time of the arrival of the steppe component (Allentoft et al., 2015). The two Late Neolithic Y. pestis genomes from the Baltic in this study were reconstructed from individuals associated with the Corded Ware Complex (Gyvakarai1 and KunilaII). The Baltic Y. pestis genomes are genetically derived from the strain that was found in the ‘Andronovo Complex’ from the Altai region [my note: I think they mean Afanasievo], suggesting that the disease might have spread with steppe pastoralists from Central Eurasia to Eastern and Central Europe during their massive range expansion. The younger Late Neolithic Y. pestis genomes from Southern Germany are genetically derived from the Baltic strains and are found in individuals associated with the Bell Beaker Complex. Previous analysis have shown that Bell Beaker individuals from Germany also carry ‘steppe ancestry (Allentoft et al., 2015; Haak et al., 2015). This suggests that Y. pestis may have been spread further southwestwards analogous to the human steppe component. The youngest of the LNBA Y. pestis genomes (RISE505), found also in the Altai region, descends from the Central European strains, and thus suggest a spread back into the eastern steppes.

Tuesday, December 13, 2016

The vast majority of patients with Nijmegen Breakage Syndrome (NBS) are of Slavic origin and carry a deleterious deletion (c.657del5; rs587776650) in the NBN gene on chromosome 8q21. This mutation is essentially confined to Slavic populations and may thus be considered a Slavic founder mutation. Notably, not a single parenthood of a homozygous c.657del5 carrier has been reported to date, while heterozygous carriers do reproduce but have an increased cancer risk. These observations seem to conflict with the considerable carrier frequency of c.657del5 of 0.5% to 1% as observed in different Slavic populations because deleterious mutations would be eliminated quite rapidly by purifying selection. Therefore, we propose that heterozygous c.657del5 carriers have increased reproductive success, i.e., that the mutation confers heterozygote advantage. In fact, in our cohort study of the reproductive history of 24 NBS pedigrees from the Czech Republic, we observed that female carriers gave birth to more children on average than female non-carriers, while no such reproductive differences were observed for males. We also estimate that c.657del5 likely occurred less than 300 generations ago, thus supporting the view that the original mutation predated the historic split and subsequent spread of the ‘Slavic people’. We surmise that the higher fertility of female c.657del5 carriers reflects a lower miscarriage rate in these women, thereby reflecting the role of the NBN gene product, nibrin, in the repair of DNA double strand breaks and their processing in immune gene rearrangements, telomere maintenance, and meiotic recombination, akin to the previously described role of the DNA repair genes BRCA1 and BRCA2.
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Of the 92 haplotypes that carried NBN c.657del5 and that could be deduced without ambiguity (S1 File), 22 (23.9%) carried identical alleles at all markers between the two most distant microsatellites D8S271 (allele 257) and D8S270 (allele 200). This haplotype (Table 8) was found in individuals from Poland, Germany, CS [Czech Republic/Slovakia] and Lusatia (Sorbs) and most likely represents the ancestral haplotype. The remaining 95 haplotypes from 40 homozygous and 15 heterozygous c.657del5 carriers (out of a total of 187 chromosomes) could not be resolved without ambiguity and are best guesses (S1 File). Among these haplotypes, we observed the putative ancestral haplotype not only in individuals from the countries mentioned above, but also from Bulgaria, Russia, and the Ukraine. Some 30% of chromosomes carrying the founder mutation showed the deduced founder haplotype (Table 8). Moreover, all 187 chromosomes carrying c.657del5 showed the same SNP alleles (Table 3). Therefore, the deletion is not only confined to individuals of Slavic origin but is most likely due to a single mutational event. All differences observed for individual microsatellite alleles are explicable by past recombination or mutation owing to the non-negligible recombination rate between the STR markers (Table 2) and the high mutation rates of microsatellites of 10−4 to 10−2 per generation.

Thursday, December 8, 2016

Scientific Reports has a new paper on the history of coat patterns in domesticated horses and the domestication process itself. Emphasis is mine:

Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in ~3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.
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In addition, we discovered that tobiano spotting, which only occurs in domestic horses and had thus far only been detected after 1500 BC, was present in the Eneolithic/Copper Age (Kazakhstan, cal. 3654–3630 BC, and Germany, cal. 3368–3101 BC). Similar to chestnut and sabino spotting, the tobiano phenotype appears to arise shortly after domestication, which is assumed to have started approximately 4000–3500 BC in the Ponto-Caspian steppe region (modern day Kazakhstan and Ukraine) [17].
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Moreover, the detection of the tobiano phenotype in two Eneolithic domestic horses from distant regions has important implications regarding the origins of horse domestication [17] and their subsequent distribution. It also supports previous claims that the emergence of domestic horses in Central Europe at the end of the fourth millennium BC was facilitated by introduced horses from the Ponto-Caspian steppe [19].

Wednesday, December 7, 2016

Abstract: The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of traits and diseases. The history of the Sardinian population has also been the focus of much research, and in recent ancient DNA (aDNA) studies, Sardinia has provided unique insight into the peopling of Europe and the spread of agriculture. In this study, we analyze whole-genome sequences of 3,514 Sardinians to address hypotheses regarding the founding of Sardinia and its relation to the peopling of Europe, including examining fine-scale substructure, population size history, and signals of admixture. We find the population of the mountainous Gennargentu region shows elevated genetic isolation with higher levels of ancestry associated with mainland Neolithic farmers and depleted ancestry associated with more recent Bronze Age Steppe migrations on the mainland. Notably, the Gennargentu region also has elevated levels of pre-Neolithic hunter-gatherer ancestry and increased affinity to Basque populations. Further, allele sharing with pre-Neolithic and Neolithic mainland populations is larger on the X chromosome compared to the autosome, providing evidence for a sex-biased demographic history in Sardinia. These results give new insight to the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.

Reporting back on the lecture on Bell Beaker by Volker Heyd this evening in Dorchester. The expected two aDNA papers on Bell Beaker have been delayed for the best possible reason. The two teams, one from Harvard and the other from Copenhagen, have agreed to amalgamate their results into one huge paper, which will give the results of over 200 samples. It is due to be published in a couple of months. Until then all the results are embargoed. Volker Heyd would only say that they are exciting.
He would also prefer me not to divulge everything he said at the lecture on the archaeological side, since he has a paper coming out in the March issue of Antiquity on Bell Beaker; while in the same issue will be one by Kristiansen on Corded Ware. So I'll be brief. He went through the various theories of the origins of Bell Beaker: the Dutch model prevalent until the 1990s, the change wrought by the Muller and Van Willigen radiocarbon date compilation of 2001 and subsequent publications of early dates in Iberia, the various attempts to make sense of an Iberian origin. The problem of the latter and of the idea of a North African origin are the same in his view. There is no prior usage of cord in pottery decoration of either. So he sticks by the Yamnaya link to a pre-BB culture proposed in Harrison and Heyd 2007. The icing on the cake lies in two significant new discoveries, which are not entirely published as yet.